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J. Biol. Chem., Vol. 277, Issue 31, 28150-28156, August 2, 2002

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Site-specific Interactions of JBP with Base and Sugar Moieties in Duplex J-DNA
EVIDENCE FOR BOTH MAJOR AND MINOR GROOVE CONTACTS^*

Robert Sabatini^§¶, Nico Meeuwenoord, Jacques H. van Boom, and Piet Borst^**

From the  Division of Geographic Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294,  Leiden Institute of Chemistry, Gorlaeus Laboratories, 2300 RA Leiden, The Netherlands, and ^** Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands

-D-Glucosyl-hydroxymethyluracil, also called base J, is an unusually modified DNA base conserved among Kinetoplastida. Base J is found predominantly in repetitive DNA and correlates with epigenetic silencing of telomeric variant surface glycoprotein genes. We have previously identified a J-binding protein (JBP) in Trypanosoma, Leishmania, and Crithidia, and we have shown that it is a structure-specific binding protein. Here we examine the molecular interactions that contribute to recognition of the glycosylated base in synthetic DNA substrates using modification interference, modification protection, DNA footprinting, and photocross-linking techniques. We find that the two primary requirements for J-DNA recognition include contacts at base J and a base immediately 5' of J (J-1). Methylation interference analysis indicates that the requirement of the base at position J-1 is due to a major groove contact independent of the sequence. DNA footprinting of the JBP·J-DNA complex with 1,10-phenanthroline-copper demonstrates that JBP contacts the minor groove at base J. Substitution of the thymine moiety of J with cytosine reduces the affinity for JBP ~15-fold. These data indicate that the sole sequence dependence for JBP binding may lie in the thymine moiety of base J and that recognition requires only two specific base contacts, base J and J-1, within both the major and minor groove of the J-DNA duplex.

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